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	   <h2>flyatlas-service.js</h2>
	
</center>

	


<h4>Summary</h4>
<p>
	
		This script defines a service class for retrieving data from flyatlas.
 <BR/><BR/><B>Version: </B>$Revision:538 $ on $Date: 2008-08-27 09:08:41 +0100 (Wed, 27 Aug 2008) $ by $Author: aliman $
 <BR/><BR/><B>Requires:</B><UL>- <a href="../../flyui/util.html#">flyui.util</a><BR/>- <a href="../../flyui/sparql/Service.html#">flyui.sparql.Service</a><BR/>- YAHOO.util.Connect
 For license terms see http://flyui.googlecode.com</UL><B>Author:</B> <a href="http://purl.org/net/aliman">Alistair Miles</a>
 <BR/>
	
</p>

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        <b>Class Summary</b>
    
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    <tr bgcolor="white" class="TableRowColor">
    <td width="15%"><b><a href="flyui/flyatlas/Assay.html">flyui.flyatlas.Assay</a></b></td>
    <td>&nbsp;</td>
    </tr>
    
    <tr bgcolor="white" class="TableRowColor">
    <td width="15%"><b><a href="flyui/flyatlas/AssayGroup.html">flyui.flyatlas.AssayGroup</a></b></td>
    <td>&nbsp;</td>
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    <tr bgcolor="white" class="TableRowColor">
    <td width="15%"><b><a href="flyui/flyatlas/Service.html">flyui.flyatlas.Service</a></b></td>
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        <pre class="sourceview"><span class="comment">/**
 * <span class="attrib">@fileoverview</span>
 * This script defines a service class for retrieving data from flyatlas.
 * <span class="attrib">@author</span> &lt;a href="http://purl.org/net/aliman"&gt;Alistair Miles&lt;/a&gt;
 * <span class="attrib">@version</span> $Revision:538 $ on $Date: 2008-08-27 09:08:41 +0100 (Wed, 27 Aug 2008) $ by $Author: aliman $
 * <span class="attrib">@requires</span> flyui.util
 * <span class="attrib">@requires</span> flyui.sparql.Service
 * <span class="attrib">@requires</span> YAHOO.util.Connect
 * For license terms see http://flyui.googlecode.com
 */</span>


flyui.namespace(<span class="literal">"flyui.flyatlas"</span>);


<span class="comment">/**
 * <span class="attrib">@class</span>
 * <span class="attrib">@extends</span> flyui.sparql.Service
 */</span>
flyui.flyatlas.Service = <span class="reserved">function</span>() {};


<span class="comment">// extend</span>
flyui.flyatlas.Service.<span class="reserved">prototype</span> = new flyui.sparql.Service();


<span class="comment">/**
 * <span class="attrib">@param</span> {String} affyId
 * <span class="attrib">@param</span> {Function} success callback will be passed an array of flyui.flyatlas.AssayGroup objects
 * <span class="attrib">@param</span> {Function} failure callback will be passed a YUI failure case response object
 * <span class="attrib">@member</span> flyui.flyatlas.Service
 * <span class="attrib">@throws</span> flyui.UnexpectedException
 */</span>
flyui.flyatlas.Service.<span class="reserved">prototype</span>.getAssaysByAffyProbeId = <span class="reserved">function</span>( affyId, success, failure ) {
    var _context = <span class="literal">"flyui.flyatlas.Service.prototype.getAssaysByAffyProbeId"</span>;
    try {
        flyui.info(<span class="literal">"request: "</span>+affyId, _context);
        var chain = flyui.chain(flyui.flyatlas.Service.responseToAssayGroups, success);
        var query = <span class="reserved">this</span>._buildQueryForGetAssaysByProbeId(affyId);
        flyui.debug(<span class="literal">"query: "</span>+query, _context);
        <span class="reserved">this</span>.postQuery(query, chain, failure);
    } catch (error) {
        throw new flyui.UnexpectedException(_context, error);
    }
};


<span class="comment">/**
 * <span class="attrib">@param</span> {String} flybaseId
 * <span class="attrib">@param</span> {Function} success callback will be passed an array of flyui.flyatlas.AssayGroup objects
 * <span class="attrib">@param</span> {Function} failure callback will be passed a YUI failure case response object
 * <span class="attrib">@member</span> flyui.flyatlas.Service
 */</span>
flyui.flyatlas.Service.<span class="reserved">prototype</span>.getAssaysByFlybaseGeneId = <span class="reserved">function</span>( flybaseId, success, failure ) {
    var _context = <span class="literal">"flyui.flyatlas.Service.prototype.getAssaysByFlybaseGeneId"</span>;
    try {
        flyui.info(<span class="literal">"request: "</span>+flybaseId, _context);
        var chain = flyui.chain(flyui.flyatlas.Service.responseToAssayGroups, success);
        var query = <span class="reserved">this</span>._buildQueryForGetAssaysByFlybaseGeneId(flybaseId);
        flyui.debug(<span class="literal">"query: "</span>+query, _context);
        <span class="reserved">this</span>.postQuery(query, chain, failure);
    } catch (error) {
        throw new flyui.UnexpectedException(_context, error);
    }
}


<span class="comment">/**
 * <span class="attrib">@param</span> {Object} response a YUI success case response object
 * <span class="attrib">@type</span> Array&lt;flyui.flyatlas.AssayGroup&gt;
 * <span class="attrib">@throws</span> flyui.UnexpectedException
 * <span class="attrib">@static</span>
 */</span>
flyui.flyatlas.Service.responseToAssayGroups = <span class="reserved">function</span>( response ) {   
    var _context = <span class="literal">"flyui.flyatlas.Service.responseToAssayGroups"</span>;   
    try {
        flyui.debug(<span class="literal">"response status: "</span>+response.status, _context); 
        flyui.debug(<span class="literal">"parsing response as json: "</span>+response.responseText, _context);
        var resultSet = YAHOO.lang.JSON.parse(response.responseText);
        flyui.debug(<span class="literal">"convert result set to an array of genes"</span>, _context);
        var groups = flyui.flyatlas.AssayGroup.newInstancesFromResultSet(resultSet);
        <span class="reserved">return</span> groups;
    } catch (error) {
        throw new flyui.UnexpectedException(_context, error);
    }
};


<span class="comment">/**
 * <span class="attrib">@private</span>
 * <span class="attrib">@param</span> {String} query
 * <span class="attrib">@type</span> String
 * <span class="attrib">@throws</span> flyui.UnexpectedException
 */</span>
flyui.flyatlas.Service.<span class="reserved">prototype</span>._buildQueryForGetAssaysByProbeId = <span class="reserved">function</span>( affyId ) {
    var _context = <span class="literal">"flyui.flyatlas.Service.prototype._buildQueryForGetAssaysByProbeId"</span>;
    try {
        
        var head =          <span class="literal">"PREFIX xs: &lt;http://www.w3.org/2001/XMLSchema#&gt; \n"</span> + 
                            <span class="literal">"PREFIX : &lt;http://purl.org/NET/flyatlas/schema#&gt; "</span>;
                    
        var body_start =    <span class="literal">"SELECT * WHERE { \n"</span> +
                            <span class="literal">"?probedata :affy_id \"</span><span class="literal">"+affyId+"</span>\<span class="literal">"^^xs:string , ?affy_id ; a :ProbeData ; \n"</span> +
                            <span class="literal">"  :fly_present ?whole_present ; \n"</span> +
                            <span class="literal">"  :fly_mean ?whole_mean ; \n"</span> +
                            <span class="literal">"  :fly_SEM ?whole_sem ; "</span>;
        
        <span class="reserved">function</span> body_part( tissue ) {
        	<span class="reserved">return</span>          <span class="literal">"  :"</span>+tissue+<span class="literal">" [ \n"</span> + 
    						<span class="literal">"    a :TissueVals ; \n"</span> +
    						<span class="literal">"    :t_change ?"</span>+tissue+<span class="literal">"_change ; \n"</span> +
    						<span class="literal">"    :mean ?"</span>+tissue+<span class="literal">"_mean ; \n"</span> +
    						<span class="literal">"    :sem ?"</span>+tissue+<span class="literal">"_sem ; \n"</span> +
    						<span class="literal">"    :present ?"</span>+tissue+<span class="literal">"_present ; \n"</span> +
    						<span class="literal">"    :ratio ?"</span>+tissue+<span class="literal">"_ratio ; \n"</span> +
    						<span class="literal">"  ] ; "</span>
        }
    
        var body_end =      <span class="literal">" . }"</span>;
        
        var query = head;
        query += body_start;
        <span class="reserved">for</span> (var i=0; i&lt;flyui.flyatlas.tissues.length; i++) { 
            var tissue = flyui.flyatlas.tissues[i];
            <span class="reserved">if</span> (tissue != <span class="literal">"whole"</span>) {
                query += body_part(flyui.flyatlas.tissues[i]); 
            }
        }
        query += body_end;
        <span class="reserved">return</span> query;

    } catch (error) {
        throw new flyui.UnexpectedException(_context, error);
    }
}

<span class="comment">/**
 * <span class="attrib">@private</span>
 * <span class="attrib">@param</span> {String} query
 * <span class="attrib">@type</span> String
 * <span class="attrib">@throws</span> flyui.UnexpectedException
 */</span>
flyui.flyatlas.Service.<span class="reserved">prototype</span>._buildQueryForGetAssaysByFlybaseGeneId = <span class="reserved">function</span>( flybaseId ) {
    var _context = <span class="literal">"flyui.flyatlas.Service.prototype._buildQueryForGetAssaysByFlybaseGeneId"</span>;
    try {
        var head =          <span class="literal">"PREFIX xs: &lt;http://www.w3.org/2001/XMLSchema#&gt; \n"</span> + 
                            <span class="literal">"PREFIX : &lt;http://purl.org/NET/flyatlas/schema#&gt; \n"</span> +
                            <span class="literal">"PREFIX fb: &lt;http://openflydata.org/id/flybase/feature/&gt; \n"</span>;
                    
        var body_start =    <span class="literal">"SELECT * WHERE { \n"</span> +
                            <span class="literal">"?probedata :gene fb:"</span>+flybaseId+<span class="literal">"; \n"</span> +
                            <span class="literal">"  a :ProbeData ; \n"</span> +
                            <span class="literal">"  :affy_id ?affy_id ; \n"</span> +
                            <span class="literal">"  :fly_present ?whole_present ; \n"</span> +
                            <span class="literal">"  :fly_mean ?whole_mean ; \n"</span> +
                            <span class="literal">"  :fly_SEM ?whole_sem ; \n"</span>;
        
        <span class="reserved">function</span> body_part( tissue ) {
        	<span class="reserved">return</span>          <span class="literal">"  :"</span>+tissue+<span class="literal">" [ \n"</span> + 
    						<span class="literal">"    a :TissueVals ; \n"</span> +
    						<span class="literal">"    :t_change ?"</span>+tissue+<span class="literal">"_change ; \n"</span> +
    						<span class="literal">"    :mean ?"</span>+tissue+<span class="literal">"_mean ; \n"</span> +
    						<span class="literal">"    :sem ?"</span>+tissue+<span class="literal">"_sem ; \n"</span> +
    						<span class="literal">"    :present ?"</span>+tissue+<span class="literal">"_present ; \n"</span> +
    						<span class="literal">"    :ratio ?"</span>+tissue+<span class="literal">"_ratio ; \n"</span> +
    						<span class="literal">"  ] ; \n"</span>
        }
    
        var body_end =      <span class="literal">" . }"</span>;
        
        var query = head;
        query += body_start;
        <span class="reserved">for</span> (var i=0; i&lt;flyui.flyatlas.tissues.length; i++) { 
            var tissue = flyui.flyatlas.tissues[i];
            <span class="reserved">if</span> (tissue != <span class="literal">"whole"</span>) {
                query += body_part(flyui.flyatlas.tissues[i]); 
            }
        }
        query += body_end;
        <span class="reserved">return</span> query;

    } catch (error) {
        throw new flyui.UnexpectedException(_context, error);
    }
}


<span class="comment">/**
 * <span class="attrib">@class</span>
 */</span>
flyui.flyatlas.AssayGroup = <span class="reserved">function</span>() {

    <span class="comment">/**
     * <span class="attrib">@type</span> String
     */</span>
    <span class="reserved">this</span>.affy_id = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.whole = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.brain = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.head = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.crop = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.midgut = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.hindgut = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.tubule = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.ovary = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.testis = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.acc = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.l_tubule = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.l_fatbody = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.ta_ganglion = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.carcass = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> flyui.flyatlas.Assay
     */</span>
    <span class="reserved">this</span>.sgland = null;
    
};


<span class="comment">/**
 * <span class="attrib">@param</span> {Object} resultSet
 * <span class="attrib">@type</span> Array&lt;flyui.flyatlas.AssayGroup&gt;
 * <span class="attrib">@throws</span> flyui.UnexpectedException
 */</span>
flyui.flyatlas.AssayGroup.newInstancesFromResultSet = <span class="reserved">function</span>( resultSet ) {
    var _context = <span class="literal">"flyui.flyatlas.AssayGroup.newInstancesFromResultSet"</span>;
    try {
    	var groups = [];
    	<span class="reserved">for</span> (var i=0; i&lt;resultSet.results.bindings.length; i++) {
    		var binding = resultSet.results.bindings[i];
    		groups[groups.length] = flyui.flyatlas.AssayGroup.newInstanceFromBinding(binding);
    	}
    	<span class="reserved">return</span> groups;
    } catch (error) {
        throw new flyui.UnexpectedException(_context, error);
    }
};


<span class="comment">/**
 * <span class="attrib">@param</span> {Object} binding
 * <span class="attrib">@type</span> flyui.flyatlas.AssayGroup
 * <span class="attrib">@throws</span> flyui.UnexpectedException
 */</span>
flyui.flyatlas.AssayGroup.newInstanceFromBinding = <span class="reserved">function</span>( binding ) {
    var _context = <span class="literal">"flyui.flyatlas.AssayGroup.newInstanceFromBinding"</span>;
    try {
    	var group = new flyui.flyatlas.AssayGroup();
    	
    	group.affy_id = binding[<span class="literal">"affy_id"</span>].value;
    	
    	<span class="comment">// populate assays</span>
    	<span class="reserved">for</span> (var i=0; i&lt;flyui.flyatlas.tissues.length; i++) {
    		var tissue = flyui.flyatlas.tissues[i];
    		group[tissue] = flyui.flyatlas.Assay.newInstanceFromBinding(binding, tissue);
    	}
    	
        <span class="reserved">return</span> group;	
    } catch (error) {
        throw new flyui.UnexpectedException(_context, error);
    }
};


<span class="comment">/**
 * <span class="attrib">@class</span>
 */</span>
flyui.flyatlas.Assay = <span class="reserved">function</span>() {

    <span class="comment">/**
     * <span class="attrib">@type</span> Number
     */</span>
    <span class="reserved">this</span>.mean = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> Number
     */</span>
    <span class="reserved">this</span>.present = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> Number
     */</span>
    <span class="reserved">this</span>.sem = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> String
     */</span>
    <span class="reserved">this</span>.change = null;
    
    <span class="comment">/**
     * <span class="attrib">@type</span> Number
     */</span>
    <span class="reserved">this</span>.ratio = null;
    
};

<span class="comment">/**
 * <span class="attrib">@param</span> {Object} binding
 * <span class="attrib">@param</span> {String} tissue
 * <span class="attrib">@type</span> flyui.flyatlas.Assay
 * <span class="attrib">@static</span>
 * <span class="attrib">@throws</span> flyui.UnexpectedException
 */</span>
flyui.flyatlas.Assay.newInstanceFromBinding = <span class="reserved">function</span>( binding, tissue ) {
    var _context = <span class="literal">"flyui.flyatlas.Assay.newInstanceFromBinding"</span>;
    try {
    	var assay = new flyui.flyatlas.Assay();
    	
    	var sharedProps = [<span class="literal">"mean"</span>, <span class="literal">"sem"</span>, <span class="literal">"present"</span>];
    	
    	<span class="comment">// populate shared props</span>
    	<span class="reserved">for</span> (var i=0; i&lt;sharedProps.length; i++) {
    		var p = sharedProps[i];
    		assay[p] = binding[tissue+<span class="literal">"_"</span>+p].value;
    	}
    
        var otherProps = [<span class="literal">"ratio"</span>, <span class="literal">"change"</span>];
        
        <span class="reserved">if</span> (tissue == <span class="literal">"whole"</span>) {
        	<span class="comment">// force prop values for whole fly</span>
            assay.ratio = 1;
            assay.change = <span class="literal">"None"</span>;    	
        }
        <span class="reserved">else</span> {
    	    <span class="reserved">for</span> (var i=0; i&lt;otherProps.length; i++) {
    	        var op = otherProps[i];
    	        <span class="reserved">if</span> (binding[tissue+<span class="literal">"_"</span>+op]) {
    	            assay[op] = binding[tissue+<span class="literal">"_"</span>+op].value;
    	        }
    	    }
        }
    
        <span class="reserved">return</span> assay;
    } catch (error) {
        throw new flyui.UnexpectedException(_context, error);
    }
};


<span class="comment">/**
 * <span class="attrib">@type</span> Array&lt;String&gt;
 */</span>
flyui.flyatlas.tissues = [
    <span class="literal">"whole"</span>,
    <span class="literal">"brain"</span>,
    <span class="literal">"head"</span>,
    <span class="literal">"crop"</span>,
    <span class="literal">"midgut"</span>,
    <span class="literal">"hindgut"</span>,
    <span class="literal">"tubule"</span>,
    <span class="literal">"ovary"</span>,
    <span class="literal">"testis"</span>,
    <span class="literal">"acc"</span>,
    <span class="literal">"l_tubule"</span>,
    <span class="literal">"l_fatbody"</span>,
    <span class="literal">"ta_ganglion"</span>,
    <span class="literal">"carcass"</span>,
    <span class="literal">"sgland"</span>
];
</pre>
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<div class="jsdoc_ctime">Documentation generated by <a href="http://jsdoc.sourceforge.net/" target="_parent">JSDoc</a> on Tue Dec  9 11:08:18 2008</div>
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